Apollo cloud does not appear to be able to understand the difference between an Aperture applibrary and a folder.
When a library is transferred onto the Apollo, it's shown in the file view as a folder… which in some sense it is, but no more than any Mac application bundle is a virtual folder containing many items.
One problem that this causes is that the thumbnail images inside the Aperture library all are shown in the Photos view in Apollo… in this case, all 40,000 of them. Because they are low-res thumbnail views, there's nothing that can be done with them and they clog up the photos view because you can't distinguish between a low-res preview and the real image.
Within the images view, there does not appear to be a way to view other than as tiled images… there's no list view showing date and image size… so how does one tell that an image is a real image or a low-res preview other than with the files view… which only shows the file name, not a preview of the image?
I'm aware that Aperture is a legacy program but it is by no means the only photo app to use bundles and many will have similar problems.